[gmx-users] free energy
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Mon Jan 11 01:02:45 CET 2010
Thanks Justin,
I am not setting any Lennard-Jones parameters to zero for part B. I put
zero charge on all atoms for Part B. (Lennard Jones parameters for B are
same as Part A).
I am using default parameters for "couple-lambda0" and "couple-lambda1".
For one of my simulation (glucose + ionic liquids) I am getting solvation
free energy 35.5 Kcal/mol.
Is it too high?
Nilesh
On Sun, January 10, 2010 1:08 pm, Justin A. Lemkul wrote:
>
>
> On 1/10/10 1:03 PM, Nilesh Dhumal wrote:
>
>> Hello Justin,
>> Should I add dum_opls no. in atom type file in which Lennard-jones
>> parameters will set to zero. OR.
>> I don't have to modify anything prog.will take care of lennard-jones
>> interactions. I have put charge zero on all atom in TYPE B.
>>
>
> You shouldn't have to do make any modifications to the topology
> whatsoever, according to the documentation. The "couple-lambda0" and
> "couple-lambda1"
> parameters should do the decoupling for you.
>
> -Justin
>
>
>> Nilesh
>>
>>
>> On Sun, January 3, 2010 12:57 pm, Justin A. Lemkul wrote:
>>
>>>
>>
>>>
>>> Nilesh Dhumal wrote:
>>>
>>>
>>>> THanks Justin.
>>>> I am using Groamcs 4.0.7 version. I will do more simulation with
>>>> more lambada value betwen 0 to 0.1.
>>>
>>> I really think this is less significant than point #1 I mentioned
>>> before. Be
>>> sure you are actually setting the relevant .mdp parameters
>>> (couple-lambda0,
>>> couple-lambda1, etc) as they will heavily influence the results.
>>> Leaving
>>> them as default (as you are doing, per the .mdp file you provided) may
>>> give you something other than what you want.
>>>
>>> And do consult the links I provided; they give excellent background
>>> on the nature of these calculations.
>>>
>>> -Justin
>>>
>>>
>>>
>>>> Thanks.
>>>> Nilesh
>>>>
>>>>
>>>>
>>>> On Sun, January 3, 2010 12:39 pm, Justin A. Lemkul wrote:
>>>>
>>>>
>>>>
>>>>> Nilesh Dhumal wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hey All,
>>>>>> I am trying to calculate the solvation free energy of glucose in
>>>>>> ionic liquids. I am getting really large value for lamda=0 in
>>>>>> vacuum and solvent as well. I am getting final solvation
>>>>>> energy value ~ 310 kJ/mol. Can you tell me where I am wrong.
>>>>>>
>>>>> There are several possibilities:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 1. Are you decoupling LJ and Coulombic interactions
>>>>> simultaneously? They
>>>>> should be done in separate steps, or else you get very large
>>>>> errors.
>>>>>
>>>>> 2. You probably need a lot more lambda points to properly define
>>>>> the curve. For strongly hydrogen-bonding solutes, you should
>>>>> probably include closely-spaced points near lambda = 0 (the
>>>>> fully-coupled state), like 0.005, 0.01, 0.015, etc. The curve from
>>>>> 0 to 0.1 will otherwise be ill-defined and prone to large errors.
>>>>>
>>>>> You also do not say which version of the code you are using. The
>>>>> free energy code has been tweaked in version 4.0 such that
>>>>> topology handling is different, and the procedure is actually
>>>>> quite a bit more streamlined, given the .mdp options.
>>>>>
>>>>> Might I recommend:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> http://www.alchemistry.org/wiki/index.php/Best_Practices
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> http://md.chem.rug.nl/education/Free-Energy_Course/index.html
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Here I have pasted the the lamda value in vacuum and solvent
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Vacuum Solvent
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 0.0 527.16 0.0 4284.769
>>>>>> 0.1 74.119 0.1 161.606
>>>>>> 0.2 37.9665 0.2 -16.3176
>>>>>> 0.3 28.748 0.3 -52.488
>>>>>> 0.4 7.555 0.4 -4.3341
>>>>>> 0.5 1.495 0.5 6.996
>>>>>> 0.6 -4.796 0.6 155.485
>>>>>> 0.7 2.361 0.7 174.20
>>>>>> 0.8 3.69 0.8 193.016
>>>>>> 0.9 5.483 0.9 201.820
>>>>>> 0.92 6.391 0.92 211.79
>>>>>> 1.0 8.887 1.0 227.79
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> For each lamda value I equibrate the system for 1ns and run the
>>>>>> dynamics for 4 ns. here is dynamics file I used. pasted the
>>>>>> topology file at the end.
>>>>>>
>>>>>>
>>>>>> title = cpeptide MD cpp =
>>>>>> /usr/bin/cpp
>>>>>> constraints = none integrator = md dt =
>>>>>> 0.001
>>>>>> ; ps !
>>>>>> nsteps = 4000000 ; total 5 ps. nstcomm = 1
>>>>>> nstxout = 50 nstvout = 0 nstfout =
>>>>>> 0
>>>>>> nstlist = 10 ns_type = grid rlist =
>>>>>> 1.0
>>>>>> rcoulomb = 1.0 rvdw = 1.4
>>>>>> coulombtype = PME
>>>>>> vdwtype = cut-off pbc = xyz
>>>>>> fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz =
>>>>>> 0 pme_order = 4 ewald_rtol = 1e-5
>>>>>> optimize_fft = yes ; Berendsen temperature coupling is on
>>>>>> Tcoupl = v-rescale tau_t = 0.1 tc-grps
>>>>>> =system ref_t = 350 ; Pressure coupling is on
>>>>>> Pcoupl = parrinello-rahman
>>>>>> pcoupltype = isotropic tau_p = 0.5
>>>>>> compressibility = 4.5e-5 ref_p = 1.0 ; Generate
>>>>>> velocites is on at 300 K. gen_vel = yes gen_temp
>>>>>> = 350.0 gen_seed =
>>>>>> 173529
>>>>>> free_energy = yes init_lambda = 0.00 sc-alpha =
>>>>>> 0.6
>>>>>> sc_power = 1
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Nilesh
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Topology file (not pasted whole because of size)
>>>>>> ;
>>>>>> ; File 'glu-ac.top' was generated
>>>>>> ; By user: ndhumal (36026)
>>>>>> ; On host: c20
>>>>>> ; At date: Tue Dec 15 15:25:07 2009
>>>>>> ;
>>>>>> ; This is your topology file
>>>>>> ; Gromacs Runs One Microsecond At Cannonball Speeds
>>>>>> ;
>>>>>> ; Include forcefield parameters
>>>>>> #include "ffoplsaa.itp"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> [ moleculetype ]
>>>>>> ; Name nrexcl
>>>>>> Protein 3
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> [ atoms ]
>>>>>> ; nr type resnr residue atom cgnr charge
>>>>>> mass typeB chargeB massB 1 opls_180 1 GUL O
>>>>>> 1
>>>>>> -0.4 15.9994
>>>>>> opls_180 0.0 15.9994 2 opls_159 1 GUL C2
>>>>>> 2
>>>>>> 0.365 12.011
>>>>>> opls_159 0.0 12.011 3 opls_159 1 GUL C3
>>>>>> 2
>>>>>> 0.205 12.011
>>>>>> opls_159 0.0 12.011 4 opls_159 1 GUL C4
>>>>>> 2
>>>>>> 0.205 12.011
>>>>>> opls_159 0.0 12.011 5 opls_159 1 GUL C5
>>>>>> 2
>>>>>> 0.205 12.011
>>>>>> opls_159 0.0 12.011 6 opls_137 1 GUL C6
>>>>>> 2
>>>>>> 0.17 12.011
>>>>>> opls_137 0.0 12.011 7 opls_159 1 GUL C7
>>>>>> 2
>>>>>> 0.145 12.011
>>>>>> opls_159 0.0 12.011 8 opls_169 1 GUL O8
>>>>>> 3
>>>>>> -0.7 15.9994
>>>>>> opls_169 0.0 15.9994 9 opls_169 1 GUL O9
>>>>>> 3
>>>>>> -0.7 15.9994
>>>>>> opls_169 0.0 15.9994 10 opls_169 1 GUL O10
>>>>>> 3
>>>>>> -0.7 15.9994
>>>>>> opls_169 0.0 15.9994 11 opls_169 1 GUL O11
>>>>>> 3
>>>>>> -0.7 15.9994
>>>>>> opls_169 0.0 15.9994 12 opls_154 1 GUL O12
>>>>>> 3
>>>>>> -0.683 15.9994
>>>>>> opls_154 0.0 15.9994 13 opls_140 1 GUL H13
>>>>>> 4
>>>>>> 0.1 1.008
>>>>>> opls_140 0.0 1.008 14 opls_140 1 GUL H14
>>>>>> 4
>>>>>> 0.06 1.008
>>>>>> opls_140 0.0 1.008 15 opls_140 1 GUL H15
>>>>>> 4
>>>>>> 0.06 1.008
>>>>>> opls_140 0.0 1.008 16 opls_140 1 GUL H16
>>>>>> 4
>>>>>> 0.06 1.008
>>>>>> opls_140 0.0 1.008 17 opls_140 1 GUL H17
>>>>>> 4
>>>>>> 0.03 1.008
>>>>>> opls_140 0.0 1.008 18 opls_155 1 GUL H18
>>>>>> 5
>>>>>> 0.435 1.008
>>>>>> opls_155 0.0 1.008 19 opls_155 1 GUL H19
>>>>>> 5
>>>>>> 0.435 1.008
>>>>>> opls_155 0.0 1.008 20 opls_155 1 GUL H20
>>>>>> 5
>>>>>> 0.435 1.008
>>>>>> opls_155 0.0 1.008 21 opls_155 1 GUL H21
>>>>>> 5
>>>>>> 0.435 1.008
>>>>>> opls_155 0.0 1.008 22 opls_140 1 GUL H22
>>>>>> 5
>>>>>> 0.06 1.008
>>>>>> opls_140 0.0 1.008 23 opls_140 1 GUL H23
>>>>>> 5
>>>>>> 0.06 1.008
>>>>>> opls_140 0.0 1.008 24 opls_155 1 GUL H24
>>>>>> 6
>>>>>> 0.418 1.008
>>>>>> opls_155 0.0 1.008 25 opls_561 2 EMI C
>>>>>> 7
>>>>>> -0.13 12.011 ;
>>>>>> qtot -0.13 26 opls_561 2 EMI C2 8 -0.13
>>>>>> 12.011 ;
>>>>>> qtot -0.26 27 opls_557 2 EMI N3 9 0.15
>>>>>> 14.0067 ;
>>>>>> qtot -0.11 28 opls_558 2 EMI C4 10 -0.11
>>>>>> 12.011 ;
>>>>>> qtot -0.22 29 opls_557 2 EMI N5 11 0.15
>>>>>> 14.0067 ;
>>>>>> qtot -0.07 30 opls_135 2 EMI C6 12 -0.17
>>>>>> 12.011 ;
>>>>>> qtot -0.24 31 opls_136 2 EMI C7 13 -0.05
>>>>>> 12.011 ;
>>>>>> qtot -0.29 32 opls_135 2 EMI C8 14 -0.17
>>>>>> 12.011 ;
>>>>>> qtot -0.46 33 opls_564 2 EMI H9 15 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot -0.25 34 opls_564 2 EMI H10 15 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot -0.04 35 opls_563 2 EMI H11 15 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.17 36 opls_140 2 EMI H12 16 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.3 37 opls_140 2 EMI H13 16 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.43 38 opls_140 2 EMI H14 16 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.56 39 opls_140 2 EMI H15 17 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.69 40 opls_140 2 EMI H16 17 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.82 41 opls_140 2 EMI H17 18 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.88 42 opls_140 2 EMI H18 18 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.94 43 opls_140 2 EMI H19 18 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1 44 opls_561 3 EMI C 19 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.87 45 opls_561 3 EMI C2 20 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.74 46 opls_557 3 EMI N3 21 0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 0.89 47 opls_558 3 EMI C4 22 -0.11
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.78 48 opls_557 3 EMI N5 23 0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 0.93 49 opls_135 3 EMI C6 24 -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.76 50 opls_136 3 EMI C7 25 -0.05
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.71 51 opls_135 3 EMI C8 26 -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.54 52 opls_564 3 EMI H9 27 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.75 53 opls_564 3 EMI H10 27 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.96 54 opls_563 3 EMI H11 27 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.17 55 opls_140 3 EMI H12 28 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.3 56 opls_140 3 EMI H13 28 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.43 57 opls_140 3 EMI H14 28 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.56 58 opls_140 3 EMI H15 29 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.69 59 opls_140 3 EMI H16 29 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.82 60 opls_140 3 EMI H17 30 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.88 61 opls_140 3 EMI H18 30 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.94 62 opls_140 3 EMI H19 30 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2 63 opls_561 4 EMI C 31 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.87 64 opls_561 4 EMI C2 32 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.74 65 opls_557 4 EMI N3 33 0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 1.89 66 opls_558 4 EMI C4 34 -0.11
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.78 67 opls_557 4 EMI N5 35 0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 1.93 68 opls_135 4 EMI C6 36 -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.76 69 opls_136 4 EMI C7 37 -0.05
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.71 70 opls_135 4 EMI C8 38 -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.54 71 opls_564 4 EMI H9 39 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.75 72 opls_564 4 EMI H10 39 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.96 73 opls_563 4 EMI H11 39 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.17 74 opls_140 4 EMI H12 40 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.3 75 opls_140 4 EMI H13 40 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.43 76 opls_140 4 EMI H14 40 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.56 77 opls_140 4 EMI H15 41 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.69 78 opls_140 4 EMI H16 41 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.82 79 opls_140 4 EMI H17 42 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.88 80 opls_140 4 EMI H18 42 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.94 81 opls_140 4 EMI H19 42 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3 82 opls_561 5 EMI C 43 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.87 83 opls_561 5 EMI C2 44 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.74 84 opls_557 5 EMI N3 45 0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 2.89 85 opls_558 5 EMI C4 46 -0.11
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.78 86 opls_557 5 EMI N5 47 0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 2.93 87 opls_135 5 EMI C6 48 -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.76 88 opls_136 5 EMI C7 49 -0.05
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.71 89 opls_135 5 EMI C8 50 -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.54 90 opls_564 5 EMI H9 51 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.75 91 opls_564 5 EMI H10 51 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.96 92 opls_563 5 EMI H11 51 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.17 93 opls_140 5 EMI H12 52 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.3 94 opls_140 5 EMI H13 52 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.43 95 opls_140 5 EMI H14 52 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.56 96 opls_140 5 EMI H15 53 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.69 97 opls_140 5 EMI H16 53 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.82 98 opls_140 5 EMI H17 54 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.88 99 opls_140 5 EMI H18 54 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.94 100 opls_140 5 EMI H19 54 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4 101 opls_561 6 EMI C 55 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 3.87 102 opls_561 6 EMI C2 56 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 3.74 103 opls_557 6 EMI N3 57 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 3.89 104 opls_558 6 EMI C4 58 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 3.78 105 opls_557 6 EMI N5 59 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 3.93 106 opls_135 6 EMI C6 60 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 3.76 107 opls_136 6 EMI C7 61 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 3.71 108 opls_135 6 EMI C8 62 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 3.54 109 opls_564 6 EMI H9 63 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.75 110 opls_564 6 EMI H10 63 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.96 111 opls_563 6 EMI H11 63 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.17 112 opls_140 6 EMI H12 64 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.3 113 opls_140 6 EMI H13 64 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.43 114 opls_140 6 EMI H14 64 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.56 115 opls_140 6 EMI H15 65 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.69 116 opls_140 6 EMI H16 65 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.82 117 opls_140 6 EMI H17 66 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.88 118 opls_140 6 EMI H18 66 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.94 119 opls_140 6 EMI H19 66 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5 120 opls_561 7 EMI C 67 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 4.87 121 opls_561 7 EMI C2 68 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 4.74 122 opls_557 7 EMI N3 69 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 4.89 123 opls_558 7 EMI C4 70 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 4.78 124 opls_557 7 EMI N5 71 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 4.93 125 opls_135 7 EMI C6 72 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 4.76 126 opls_136 7 EMI C7 73 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 4.71 127 opls_135 7 EMI C8 74 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 4.54 128 opls_564 7 EMI H9 75 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.75 129 opls_564 7 EMI H10 75 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.96 130 opls_563 7 EMI H11 75 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.17 131 opls_140 7 EMI H12 76 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.3 132 opls_140 7 EMI H13 76 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.43 133 opls_140 7 EMI H14 76 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.56 134 opls_140 7 EMI H15 77 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.69 135 opls_140 7 EMI H16 77 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.82 136 opls_140 7 EMI H17 78 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.88 137 opls_140 7 EMI H18 78 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.94 138 opls_140 7 EMI H19 78 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6 139 opls_561 8 EMI C 79 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 5.87 140 opls_561 8 EMI C2 80 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 5.74 141 opls_557 8 EMI N3 81 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 5.89 142 opls_558 8 EMI C4 82 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 5.78 143 opls_557 8 EMI N5 83 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 5.93 144 opls_135 8 EMI C6 84 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 5.76 145 opls_136 8 EMI C7 85 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 5.71 146 opls_135 8 EMI C8 86 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 5.54 147 opls_564 8 EMI H9 87 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.75 148 opls_564 8 EMI H10 87 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.96 149 opls_563 8 EMI H11 87 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.17 150 opls_140 8 EMI H12 88 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.3 151 opls_140 8 EMI H13 88 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.43 152 opls_140 8 EMI H14 88 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.56 153 opls_140 8 EMI H15 89 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.69 154 opls_140 8 EMI H16 89 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.82 155 opls_140 8 EMI H17 90 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.88 156 opls_140 8 EMI H18 90 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.94 157 opls_140 8 EMI H19 90 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7 158 opls_561 9 EMI C 91 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 6.87 159 opls_561 9 EMI C2 92 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 6.74 160 opls_557 9 EMI N3 93 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 6.89 161 opls_558 9 EMI C4 94 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 6.78 162 opls_557 9 EMI N5 95 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 6.93 163 opls_135 9 EMI C6 96 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 6.76 164 opls_136 9 EMI C7 97 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 6.71 165 opls_135 9 EMI C8 98 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 6.54 166 opls_564 9 EMI H9 99 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.75 167 opls_564 9 EMI H10 99 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.96 168 opls_563 9 EMI H11 99 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.17 169 opls_140 9 EMI H12 100 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.3 170 opls_140 9 EMI H13 100 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.43 171 opls_140 9 EMI H14 100 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.56 172 opls_140 9 EMI H15 101 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.69 173 opls_140 9 EMI H16 101 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.82 174 opls_140 9 EMI H17 102 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.88 175 opls_140 9 EMI H18 102 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.94 176 opls_140 9 EMI H19 102 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8 177 opls_561 10 EMI C 103 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 7.87 178 opls_561 10 EMI C2 104 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 7.74 179 opls_557 10 EMI N3 105 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 7.89 180 opls_558 10 EMI C4 106 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 7.78 181 opls_557 10 EMI N5 107 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 7.93 182 opls_135 10 EMI C6 108 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 7.76 183 opls_136 10 EMI C7 109 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 7.71 184 opls_135 10 EMI C8 110 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 7.54 185 opls_564 10 EMI H9 111 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.75 186 opls_564 10 EMI H10 111 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.96 187 opls_563 10 EMI H11 111 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.17 188 opls_140 10 EMI H12 112 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.3 189 opls_140 10 EMI H13 112 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.43 190 opls_140 10 EMI H14 112 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.56 191 opls_140 10 EMI H15 113 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.69 192 opls_140 10 EMI H16 113 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.82 193 opls_140 10 EMI H17 114 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.88 194 opls_140 10 EMI H18 114 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.94 195 opls_140 10 EMI H19 114 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9 196 opls_561 11 EMI C 115 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 8.87 197 opls_561 11 EMI C2 116 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 8.74 198 opls_557 11 EMI N3 117 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 8.89 199 opls_558 11 EMI C4 118 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 8.78 200 opls_557 11 EMI N5 119 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 8.93 201 opls_135 11 EMI C6 120 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 8.76 202 opls_136 11 EMI C7 121 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 8.71 203 opls_135 11 EMI C8 122 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 8.54 204 opls_564 11 EMI H9 123 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.75 205 opls_564 11 EMI H10 123 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.96 206 opls_563 11 EMI H11 123 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.17 207 opls_140 11 EMI H12 124 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.3 208 opls_140 11 EMI H13 124 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.43 209 opls_140 11 EMI H14 124 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.56 210 opls_140 11 EMI H15 125 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.69 211 opls_140 11 EMI H16 125 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.82 212 opls_140 11 EMI H17 126 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.88 213 opls_140 11 EMI H18 126 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.94 214 opls_140 11 EMI H19 126 0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 10 215 opls_561 12 EMI C 127 -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 9.87 216 opls_561 12 EMI C2 128 -0.13
>>>>>> 12.011 ;
>>>>>> qtot 9.74 217 opls_557 12 EMI N3 129 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 9.89 218 opls_558 12 EMI C4 130 -0.11
>>>>>> 12.011 ;
>>>>>> qtot 9.78 219 opls_557 12 EMI N5 131 0.15
>>>>>> 14.0067 ;
>>>>>> qtot 9.93 220 opls_135 12 EMI C6 132 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 9.76 221 opls_136 12 EMI C7 133 -0.05
>>>>>> 12.011 ;
>>>>>> qtot 9.71 222 opls_135 12 EMI C8 134 -0.17
>>>>>> 12.011 ;
>>>>>> qtot 9.54 223 opls_564 12 EMI H9 135 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.75 224 opls_564 12 EMI H10 135 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.96 225 opls_563 12 EMI H11 135 0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 10.17 226 opls_140 12 EMI H12 136 0.13
>>>>>> 1.008 ;
>>>>>> qtot 10.3 227 opls_140 12 EMI H13 136 0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 10.43 228 opls_140 12 EMI H14 136 0.13
>>>>>> 1.008 ;
>>>>>> qtot 10.56 229 opls_140 12 EMI H15 137 0.13
>>>>>> 1.008 ;
>>>>>> qtot 10.69 230 opls_140 12 EMI H16 137 0.13
>>>>>> 1.008 ;
>>>>>> qtot 10.82 231 opls_140 12 EMI H17 138 0.06
>>>>>> 1.008 ;
>>>>>> qtot 10.88 232 opls_140 12 EMI H18 138 0.06
>>>>>> 1.008 ;
>>>>>> qtot 10.94 233 opls_140 12 EMI H19 138 0.06
>>>>>> 1.008 ;
>>>>>> qtot 11
>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> MILES-IGERT Trainee
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>> posting! Please don't post (un)subscribe requests to the list. Use
>>>>> the www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't
>>>>> post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>>
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting! Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org. Can't
>>> post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> ========================================
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
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